INTRODUCTION TO BIOINFORMATICS

Group Members
1. Namuhubembe Melisa Grace
2. Odong Sam
3. Lomokol Jonathan
4. Ntanda Rashid
5. Aheirwe Norbert
 PRESENTATION CONTENT

Overview of the Human Genome

Bioinformatics; An interdisciplinary field
Sequence Alignment
Pairwise Sequence Alignment
Dynamic Programming
Global Alignment
Local Alignment and BLAST
Other Bioinformatics Tools and Resources
Bioinformatics Databases
Next Generation Sequencing
 OVERVIEW OF THE HUMAN GENOME

• The human genome, consisting of approximately 3.1 billion base pairs,

serves as the instruction manual for life.
• It is composed of four nucleotides: Adenine (A), Thymine (T), Cytosine (C),
and Guanine (G).
• Around 2.9% of the genome comprises genes responsible for encoding
proteins.
• These seemingly simple sequences hold the key to unraveling the mysteries
of life and understanding evolutionary processes.
• Bioinformatics plays a crucial role in sequencing and analyzing genomes of
various organisms.
 BIOINFORMATICS: AN INTERDISCIPLINARY FIELD

• Bioinformatics is an interdisciplinary field that combines

biology, computer science, and statistics.

• It involves the development and application of computational

tools and techniques to solve biological problems.

• Numerous online bioinformatics tools, with user-friendly

interfaces and tutorials, are freely available to biologists.

• However, it is essential to grasp the underlying principles of

these tools to utilize them effectively.

• Understanding the assumptions and methodologies behind

the tools ensures accurate analysis and interpretation.
 SEQUENCE ALIGNMENT

• Sequence alignment is a fundamental technique for comparing and identifying similarities

between DNA or protein sequences.

• It is used to determine the alignment between two given sequences (S1 and S2).

• The similarity between amino acids in the sequences is assessed using a substitution
matrix, such as BLOSUM62.

• The goal is to find the optimal alignment that maximizes the scoring function, which
quantifies the quality of alignment.

• Traditional enumeration-based methods are theoretically feasible but impractical for

large-scale applications, necessitating faster algorithms.
 PAIRWISE SEQUENCE ALIGNMENT

• Pairwise sequence alignment is a specific type of sequence alignment

used to align two given sequences.

• It is used to compare and identify similarities between sequences, such as

DNA or protein sequences.

• The alignment process considers the similarity between amino acids in the
sequences using a substitution matrix.

• The optimal alignment is determined by maximizing the scoring function,

which quantifies the quality of alignment.

• Dynamic programming algorithms, such as the Needleman-Wunsch

algorithm, are commonly used for pairwise sequence alignment.
 DYNAMIC PROGRAMMING

• Dynamic programming is a problem-solving technique used in various fields, including

bioinformatics.

• It solves complex problems by breaking them down into smaller overlapping subproblems.

• The solution to each subproblem is stored and reused to solve larger subproblems, leading to an
optimal solution.

• In sequence alignment, dynamic programming is used to find the optimal alignment by iteratively
filling a matrix.

• The Needleman-Wunsch algorithm, based on dynamic programming, efficiently performs global

sequence alignment.
 GLOBAL ALIGNMENT

• Global Sequence Alignment is a type of sequence alignment

that aligns two sequences along their entire length.

• It is used to align closely related sequences, such as

homologous genes or proteins with similar functions.

• The Needleman-Wunsch algorithm is a widely used

algorithm for global sequence alignment.

• The algorithm considers user-defined scoring functions and

uses dynamic programming principles.

• It identifies regions of similarity and produces an alignment

that maximizes the overall score.
 LOCAL ALIGNMENT AND BLAST

• Local Sequence Alignment is used to identify short, similar

regions between two sequences.

• The algorithm, such as the Smith-Waterman algorithm, detects

significant local alignments.

• Basic Local Alignment Search Tool (BLAST) is a widely used

bioinformatics tool for local alignment searches.

• BLAST employs heuristics and indexing techniques to

efficiently search large databases for similar sequences.

• It provides valuable insights into evolutionary relationships,

functional annotations, and protein structure predictions.
 OTHER BIOINFORMATICS TOOLS AND RESOURCES

• Multiple sequence alignment tools, such as Clustal Omega and

MUSCLE, align three or more sequences simultaneously.

• Phylogenetic analysis tools, like PhyML and MrBayes,

reconstruct evolutionary relationships based on sequence data.

• Structure prediction tools, including I-TASSER and SWISS-

MODEL, predict the 3D structure of proteins.

• Functional annotation tools, such as DAVID and PANTHER,

provide functional information about genes and proteins.

• Data visualization tools, such as R and Python libraries,

facilitate data exploration and presentation.
 BIOINFORMATICS DATABASES

• Bioinformatics databases store, organize, and provide access to

vast amounts of biological data for research and analysis.

• These databases contain diverse information, including DNA and

protein sequences, gene expression data, metabolic pathways, and
genetic variations.

• Integration of data from multiple sources enables comprehensive

analyses
 NEXT GENERATION SEQUENCING (NGS)

• Next Generation Sequencing (NGS) technologies have

revolutionized DNA sequencing by generating a vast amount of data.

• Over 1000 NGS sequencers are available worldwide, surpassing the

capabilities of the Sanger sequencing method.

• NGS, also known as deep sequencing, produces shorter reads with

higher error rates compared to traditional methods.

• NGS has facilitated research in genomic DNA sequencing,

epigenetic modifications, transcriptomes, and protein-DNA
interactions.
Thank You